From 3d3bac74b995e6b704c64dd20f8d80176fd760c5 Mon Sep 17 00:00:00 2001
From: Tobias Meisel <tobias.meisel@ufz.de>
Date: Thu, 22 Jul 2021 11:23:52 +0200
Subject: [PATCH] [MeL/IO] XDMF/HDF5: Review follow up
---
MeshLib/IO/XDMF/XdmfHdfWriter.cpp | 30 +++++++++++++-----------
MeshLib/IO/XDMF/XdmfHdfWriter.h | 2 +-
MeshLib/IO/XDMF/XdmfWriter.cpp | 4 ++--
MeshLib/IO/XDMF/XdmfWriter.h | 2 +-
MeshLib/IO/XDMF/transformData.cpp | 10 ++++----
MeshLib/IO/XDMF/writeXdmf.cpp | 39 +++++++++++++++----------------
MeshLib/IO/writeMeshToFile.cpp | 2 +-
ProcessLib/Output/Output.cpp | 20 +++++++---------
8 files changed, 55 insertions(+), 54 deletions(-)
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
index c3f3abd6f79..c84c0fe906d 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
@@ -42,10 +42,12 @@ XdmfHdfWriter::XdmfHdfWriter(MeshLib::Mesh const& mesh,
// list
std::function<bool(HdfData)> is_variable_hdf_attribute =
[&variable_output_names](
- bool outputnames) -> std::function<bool(HdfData)> {
+ bool outputnames) -> std::function<bool(HdfData)>
+ {
if (outputnames)
{
- return [&variable_output_names](HdfData data) -> bool {
+ return [&variable_output_names](HdfData data) -> bool
+ {
return std::find(variable_output_names.begin(),
variable_output_names.end(),
data.name) != variable_output_names.end();
@@ -88,17 +90,19 @@ XdmfHdfWriter::XdmfHdfWriter(MeshLib::Mesh const& mesh,
std::vector<XdmfData> xdmf_attributes;
std::transform(attributes.begin(), attributes.end(),
std::back_inserter(xdmf_attributes),
- [&attributes](AttributeMeta& att) -> XdmfData
- {
- size_t const i = &att - &attributes.front();
- // index 1 geo, index 2 topology, attributes start at
- // index 3
- att.xdmf.index = i + 4;
- return att.xdmf;
- });
+ [](AttributeMeta const& att) -> XdmfData
+ { return att.xdmf; });
+
+ for (size_t i = 0; i < attributes.size(); ++i)
+ {
+ // index 1 time, index 2 geo, index 3 topology, attributes start at
+ // index 4
+ xdmf_attributes[i].index = i + 4;
+ }
std::function<bool(XdmfData)> is_variable_xdmf_attribute =
- [&variable_output_names](XdmfData data) -> bool {
+ [&variable_output_names](XdmfData data) -> bool
+ {
return std::find(variable_output_names.begin(),
variable_output_names.end(),
data.name) != variable_output_names.end();
@@ -125,8 +129,8 @@ XdmfHdfWriter::XdmfHdfWriter(MeshLib::Mesh const& mesh,
}
}
-void XdmfHdfWriter::writeStep([[maybe_unused]] int const& time_step,
- double const& time)
+void XdmfHdfWriter::writeStep([[maybe_unused]] int const time_step,
+ double const time)
{
// ToDo (tm) time_step will be used for simulation continuation (restart)
_hdf_writer->writeStep();
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.h b/MeshLib/IO/XDMF/XdmfHdfWriter.h
index d4301f0b7ab..bf843dd5014 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.h
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.h
@@ -48,7 +48,7 @@ public:
* @param time_step number of the step (temporal collection)
* @param time time value of the current time_step
*/
- void writeStep(int const& time_step, double const& time);
+ void writeStep(int time_step, double time);
private:
// hdf_writer must be destructed before xdmf_writer
diff --git a/MeshLib/IO/XDMF/XdmfWriter.cpp b/MeshLib/IO/XDMF/XdmfWriter.cpp
index 222dca5d209..67ffb7cc669 100644
--- a/MeshLib/IO/XDMF/XdmfWriter.cpp
+++ b/MeshLib/IO/XDMF/XdmfWriter.cpp
@@ -8,10 +8,10 @@
namespace MeshLib::IO
{
-XdmfWriter::XdmfWriter(std::string const& xdmf_filename,
+XdmfWriter::XdmfWriter(std::string xdmf_filename,
std::function<std::string(std::vector<double>)>
xdmf_writer_fn)
- : filename(xdmf_filename), xdmf_writer(xdmf_writer_fn)
+ : filename(std::move(xdmf_filename)), xdmf_writer(xdmf_writer_fn)
{
}
diff --git a/MeshLib/IO/XDMF/XdmfWriter.h b/MeshLib/IO/XDMF/XdmfWriter.h
index c5b675cc192..2cd65b1ee2d 100644
--- a/MeshLib/IO/XDMF/XdmfWriter.h
+++ b/MeshLib/IO/XDMF/XdmfWriter.h
@@ -25,7 +25,7 @@ public:
* @param xdmf_filename absolute or relative filepath to the xdmf file
* @param xdmf_writer_fn function that generates xdmf string
*/
- XdmfWriter(std::string const& xdmf_filename,
+ XdmfWriter(std::string xdmf_filename,
std::function<std::string(std::vector<double>)>
xdmf_writer_fn);
XdmfWriter(XdmfWriter&&) = default;
diff --git a/MeshLib/IO/XDMF/transformData.cpp b/MeshLib/IO/XDMF/transformData.cpp
index d8179c8f34e..734b41c79a1 100644
--- a/MeshLib/IO/XDMF/transformData.cpp
+++ b/MeshLib/IO/XDMF/transformData.cpp
@@ -36,7 +36,7 @@ struct XdmfTopology
unsigned int number_of_nodes;
};
-constexpr auto elemOGSTypeToXDMFType()
+static constexpr auto elemOGSTypeToXDMFType()
{
std::array<XdmfTopology, to_underlying(MeshLib::CellType::enum_length)>
elem_type{};
@@ -62,9 +62,10 @@ constexpr auto elemOGSTypeToXDMFType()
return elem_type;
}
-auto cellTypeOGS2XDMF(MeshLib::CellType const& cell_type)
+constexpr auto elem_type_ogs2xdmf = elemOGSTypeToXDMFType();
+
+constexpr auto cellTypeOGS2XDMF(MeshLib::CellType const& cell_type)
{
- constexpr auto elem_type_ogs2xdmf = elemOGSTypeToXDMFType();
return elem_type_ogs2xdmf[to_underlying(cell_type)];
}
@@ -80,7 +81,8 @@ std::optional<AttributeMeta> transformAttribute(
// (and overwrites) data that can only be collected via the typed property.
// It has boolean return type to allow kind of pipe using || operator.
auto f = [&data_type, &num_of_tuples, &data_ptr,
- &property_pair](auto basic_type) -> bool {
+ &property_pair](auto basic_type) -> bool
+ {
auto const property_base = property_pair.second;
auto const typed_property =
dynamic_cast<PropertyVector<decltype(basic_type)> const*>(
diff --git a/MeshLib/IO/XDMF/writeXdmf.cpp b/MeshLib/IO/XDMF/writeXdmf.cpp
index 0310d83a9cd..5829ba8483c 100644
--- a/MeshLib/IO/XDMF/writeXdmf.cpp
+++ b/MeshLib/IO/XDMF/writeXdmf.cpp
@@ -6,6 +6,7 @@
#include <spdlog/fmt/bundled/format.h>
#include <algorithm>
+#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
@@ -15,6 +16,7 @@
#include <string_view>
#include <vector>
+#include "BaseLib/Error.h"
#include "BaseLib/cpp23.h"
#include "MeshLib/Location.h"
@@ -34,18 +36,14 @@ constexpr char const* mesh_item_type_strings[] = {"Node", "Edge", "Face",
"Cell", "IntegrationPoint"};
// Transforms MeshItemType into string
-static std::string mesh_item_type_string(
+static std::string meshItemTypeString(
std::optional<MeshItemType> const& item_type)
{
- /// Char array names for all of MeshItemType values.
if (item_type)
{
return mesh_item_type_strings[static_cast<int>(item_type.value())];
}
- else
- {
- return "";
- }
+ OGS_FATAL("Cannot convert an empty optional mesh item type.");
}
// Transforms MeshPropertyDataType into string
@@ -69,8 +67,7 @@ static auto meshPropertyDatatypeString()
static std::string getPropertyDataTypeString(
MeshPropertyDataType const& ogs_data_type)
{
- auto ogs_to_xdmf_type = meshPropertyDatatypeString();
- return ogs_to_xdmf_type[to_underlying(ogs_data_type)];
+ return meshPropertyDatatypeString()[to_underlying(ogs_data_type)];
}
// Returns MeshPropertyDataType-to-Size (in bytes) lookup-table
@@ -89,11 +86,12 @@ static constexpr auto meshPropertyDatatypeSize()
return property_sizes;
}
+inline auto ogs_to_xdmf_type = meshPropertyDatatypeSize();
+
// Transform MeshPropertyDataType into type_sizes (in bytes)
static std::string getPropertyDataTypeSize(
MeshPropertyDataType const& ogs_data_type)
{
- constexpr auto ogs_to_xdmf_type = meshPropertyDatatypeSize();
return fmt::format("{}", ogs_to_xdmf_type[to_underlying(ogs_data_type)]);
}
@@ -148,7 +146,7 @@ std::function<std::string(std::vector<double>)> write_xdmf(
return [join, transform](auto const& collection)
{
std::vector<std::string> temp;
- temp.resize(collection.size());
+ temp.reserve(collection.size());
std::transform(collection.begin(), collection.end(),
std::back_inserter(temp), transform);
return join(temp);
@@ -175,7 +173,7 @@ std::function<std::string(std::vector<double>)> write_xdmf(
"ElementDegree=\"0\" "
"ElementFamily=\"\" ItemType=\"\" Name=\"{name}\" "
"Type=\"None\">{dataitem}\n\t</Attribute>",
- "center"_a = mesh_item_type_string(attribute.attribute_center),
+ "center"_a = meshItemTypeString(attribute.attribute_center),
"name"_a = attribute.name,
"dataitem"_a = dataitem_transform(attribute));
};
@@ -235,7 +233,7 @@ std::function<std::string(std::vector<double>)> write_xdmf(
variable, time_step, max_step, h5filename](XdmfData const& attr)
{
// new data arrived
- bool changed =
+ bool const changed =
((time_step > 0 && (variable == time_attribute::variable)) ||
time_step == 0);
if (changed)
@@ -246,8 +244,8 @@ std::function<std::string(std::vector<double>)> write_xdmf(
}
else
{
- std::vector<unsigned int> d = {1, 1, 2, 1, attr.index};
- return pointer_transfrom(d);
+ std::array<unsigned int, 5> position = {1, 1, 2, 1, attr.index};
+ return pointer_transfrom(position);
};
};
};
@@ -297,7 +295,7 @@ std::function<std::string(std::vector<double>)> write_xdmf(
// c++20 ranges zip missing
auto const max_step = times.size();
std::vector<std::string> grids;
- grids.resize(max_step);
+ grids.reserve(max_step);
for (size_t time_step = 0; time_step < max_step; ++time_step)
{
grids.push_back(time_grid_transform(
@@ -312,15 +310,16 @@ std::function<std::string(std::vector<double>)> write_xdmf(
// Generator function that return a function that represents complete xdmf
// structure
- auto const xdmf_writer_fn =
- [temporal_grid_collection_transform](
- auto const& ogs_version, auto const& geometry, auto const& topology,
- auto const& constant_attributes, auto const& variable_attributes)
+ auto const xdmf_writer_fn = [temporal_grid_collection_transform](
+ auto ogs_version, auto geometry,
+ auto topology, auto constant_attributes,
+ auto variable_attributes)
{
// This function will be the return of the surrounding named function
// capture by copy - it is the function that will survive this scope!!
// Use generalized lambda capture to move for optimization
- return [temporal_grid_collection_transform, ogs_version,
+ return [temporal_grid_collection_transform,
+ ogs_version = std::move(ogs_version),
geometry = std::move(geometry), topology = std::move(topology),
constant_attributes = std::move(constant_attributes),
variable_attributes = std::move(variable_attributes)](
diff --git a/MeshLib/IO/writeMeshToFile.cpp b/MeshLib/IO/writeMeshToFile.cpp
index 34af711a711..3574308774f 100644
--- a/MeshLib/IO/writeMeshToFile.cpp
+++ b/MeshLib/IO/writeMeshToFile.cpp
@@ -50,7 +50,7 @@ int writeMeshToFile(const MeshLib::Mesh& mesh,
return 0;
}
ERR("writeMeshToFile(): Unknown file extension '{:s}'. Can not write file "
- "'{'s}'.",
+ "'{:s}'.",
file_path.extension().string(), file_path.string());
return 0;
}
diff --git a/ProcessLib/Output/Output.cpp b/ProcessLib/Output/Output.cpp
index cc960786e3b..d1340797473 100644
--- a/ProcessLib/Output/Output.cpp
+++ b/ProcessLib/Output/Output.cpp
@@ -179,7 +179,8 @@ struct Output::OutputFile
std::string const& prefix, std::string const& suffix,
std::string const& mesh_name, int const timestep, double const t,
int const iteration, int const data_mode_,
- bool const compression_, std::set<std::string> const& outputnames)
+ bool const compression_,
+ std::set<std::string> const& outputnames)
: name(constructFilename(type, prefix, suffix, mesh_name, timestep, t,
iteration)),
path(BaseLib::joinPaths(directory, name)),
@@ -307,7 +308,8 @@ void Output::doOutputAlways(Process const& process,
return;
}
- auto output_bulk_mesh = [&](MeshLib::Mesh const& mesh) {
+ auto output_bulk_mesh = [&](MeshLib::Mesh const& mesh)
+ {
MeshLib::IO::PVDFile* pvd_file = nullptr;
if (_output_file_type == ProcessLib::OutputType::vtk)
{
@@ -322,7 +324,6 @@ void Output::doOutputAlways(Process const& process,
}
else if (_output_file_type == ProcessLib::OutputType::xdmf)
{
-
OutputFile const file(
_output_directory, _output_file_type, _output_file_prefix, "",
mesh.getName(), timestep, t, iteration, _output_file_data_mode,
@@ -330,9 +331,6 @@ void Output::doOutputAlways(Process const& process,
_output_data_specification.output_variables);
outputMeshXdmf(file, mesh, timestep, t);
-
-
-
}
};
@@ -347,9 +345,8 @@ void Output::doOutputAlways(Process const& process,
// mesh related output
auto& non_bulk_mesh = *BaseLib::findElementOrError(
begin(_meshes), end(_meshes),
- [&mesh_output_name](auto const& m) {
- return m->getName() == mesh_output_name;
- },
+ [&mesh_output_name](auto const& m)
+ { return m->getName() == mesh_output_name; },
"Need mesh '" + mesh_output_name + "' for the output.");
std::vector<MeshLib::Node*> const& nodes = non_bulk_mesh.getNodes();
@@ -370,9 +367,8 @@ void Output::doOutputAlways(Process const& process,
mesh_dof_table_pointers.reserve(mesh_dof_tables.size());
transform(cbegin(mesh_dof_tables), cend(mesh_dof_tables),
back_inserter(mesh_dof_table_pointers),
- [](std::unique_ptr<NumLib::LocalToGlobalIndexMap> const& p) {
- return p.get();
- });
+ [](std::unique_ptr<NumLib::LocalToGlobalIndexMap> const& p)
+ { return p.get(); });
output_secondary_variable = false;
addProcessDataToMesh(
--
GitLab